Mediator-associated proteins and the small RNA–guided Polycomb repressive complex enhance cryptic transcription for transposon exclusion

Suppression of transposable elements (TEs) is critical for maintaining genome integrity. The evolutionary arms race between TEs and their eukaryotic host organisms has driven the development of small RNA–dependent mechanisms that specifically suppress TEs while leaving non-TE regions unperturbed. In the binucleated ciliate Tetrahymena , small RNAs (sRNAs) are generated from both TE and non-TE regions of the germline genome, whereas noncoding RNAs (ncRNAs) from the TE-free somatic genome target and eliminate non-TE sRNAs, thereby selectively preserving TE-specific sRNAs for guiding TE recognition. Since sRNAs are produced from both strands, the counteracting ncRNAs must also occur bidirectionally. However, the mechanism by which the somatic genome generates ncRNAs from both strands remains unresolved. Here, we show that these ncRNAs arise from widespread cryptic transcription initiated outside canonical promoters and dependent on the developmentally specific Mediator complex–associated proteins Dima1 and Emit2. We further demonstrate that sRNA-guided recruitment of the Tetrahymena Polycomb repressive complex 2 and Dima1 occupancy are mutually reinforcing, promoting local accumulation of RNA polymerase II, which may facilitate cryptic transcription from these loci in a histone methyltransferase-independent manner. Disruption of Dima1 abolishes cryptic transcription, leads to aberrant accumulation of non-TE sRNAs, and results in erroneous genome elimination and cell death. These findings reveal a regulatory circuit involving sRNAs, Polycomb, and the Mediator-associated protein Dima1 that promotes cryptic transcription, thereby ensuring accurate TE exclusion and genome integrity.